Comparison of Material Consumption, Experimental Protocols and Computation Time in DNA Computing

N. Rajaee, K. Hong Ping, A. Lit, D. N. S. A. Salleh, and L. Y. Ng

Abstract—One of the major constraints in DNA computation
is the exponential increase in material consumption and
computation time for larger computation size in DNA computing
particularly in critical stages such as initial pool generation and
extraction during gel electrophoresis. In DNA computation,
both the hybridization-ligation method and parallel overlap
assembly method can be utilized to generate the initial pool of all
possible solutions. In this paper, we discuss and compare the
implementation of N × N Boolean matrix multiplication via in
vitro implementation between Hybridization-Ligation Method
and Parallel Overlap Assembly Method to show that selection of
tools and protocols affect the cost effectiveness of a computation
in terms of the material consumption, protocol steps and
execution time to compute. In general, the the parallel overlap
assembly method performs better than hybridization-ligation
method in terms of the three parameters mentioned. The
calculations are based on approximation of unique sequence
strands required for the computation and not actual calculations
on the nmol concentration. 